title: G-Quadruplex conformational change driven by pH variation with potential application as a nanoswitch.
abstract: BACKGROUND
  G-Quadruplex is a highly polymorphic structure, and its behavior in acidic condition has not been well studied.
  
  
  METHODS
  Circular dichroism (CD) spectra were used to study the conformational change of G-quadruplex. The thermal stabilities of the G-quadruplex were measured with CD melting. Interconversion kinetics profiles were investigated by using CD kinetics. The fluorescence of the inserted 2-Aminopurine (Ap) was monitored during pH change and acrylamide quenching, indicating the status of the loop. Proton NMR was adopted to help illustrate the change of the conformation.
  
  
  RESULTS
  G-Quadruplex of specific loop was found to be able to transform upon pH variation. The transformation was resulted from the loop rearrangement. After screening of a library of diverse G-quadruplex, a sequence exhibiting the best transformation property was found. A pH-driven nanoswitch with three gears was obtained based on this transition cycle.
  
  
  CONCLUSIONS
  Certain G-quadruplex was found to go through conformational change at low pH. Loop was the decisive factor controlling the interconversion upon pH variation. G-Quadruplex with TT central loop could be converted in a much milder condition than the one with TTA loop. It can be used to design pH-driven nanodevices such as a nanoswitch.
  
  
  CONCLUSIONS
  These results provide more insights into G-quadruplex polymorphism, and also contribute to the design of DNA-based nanomachines and logic gates.
authors.affiliation: School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China.
authors.forename: Yi-Yong
authors.initials: YY
authors.lastname: Yan
authors.forename: Jia-Heng
authors.initials: JH
authors.lastname: Tan
authors.forename: Yu-Jing
authors.initials: YJ
authors.lastname: Lu
authors.forename: Siu-Cheong
authors.initials: SC
authors.lastname: Yan
authors.forename: Kwok-Yin
authors.initials: KY
authors.lastname: Wong
authors.forename: Ding
authors.initials: D
authors.lastname: Li
authors.forename: Lian-Quan
authors.initials: LQ
authors.lastname: Gu
authors.forename: Zhi-Shu
authors.initials: ZS
authors.lastname: Huang
mesh_terms: D054856:G-Quadruplexes; D006863:Hydrogen-Ion Concentration; D036103:Nanotechnology; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation
keywords: Acidic pH; Conformational interconversion; G-Quadruplex; Nanoswitch; Thiazole orange (TO); pH-driven